메뉴 건너뛰기




Volumn 50, Issue 11, 2011, Pages 1857-1863

Enhanced base-pair opening in the adenine tract of a RNA double helix

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE TRACTS; AMMONIA CONCENTRATIONS; BASE PAIRS; DNA DUPLEXES; DOUBLE HELIX; EXCHANGE RATES; IMINO PROTONS; OPENING REACTIONS; PROTON EXCHANGE; RNA DUPLEXES;

EID: 79952793757     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi1014997     Document Type: Article
Times cited : (15)

References (33)
  • 1
    • 0032167569 scopus 로고    scopus 로고
    • Distinct frequency-distributions of homopolymeric DNA tracts in different genomes
    • Dechering, K. J., Cuelenaere, K., Konings, R. N. H., and Leunissen, J. A. M. (1998) Distinct frequency-distributions of homopolymeric DNA tracts in different genomes Nucleic Acids Res. 26, 4056-4062 (Pubitemid 28401361)
    • (1998) Nucleic Acids Research , vol.26 , Issue.17 , pp. 4056-4062
    • Dechering, K.J.1    Cuelenaere, K.2    Konings, R.N.H.3    Leunissen, J.A.M.4
  • 2
    • 67649710352 scopus 로고    scopus 로고
    • The unique structure of A-tracts and intrinsic DNA bending
    • Haran, T. E. and Mohanty, U. (2009) The unique structure of A-tracts and intrinsic DNA bending Q. Rev. Biophys. 42, 41-81
    • (2009) Q. Rev. Biophys. , vol.42 , pp. 41-81
    • Haran, T.E.1    Mohanty, U.2
  • 3
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:dT) tracts: Major determinants of nucleosome organization
    • Segal, E. and Widom, J. (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization Curr. Opin. Struct. Biol. 19, 65-71
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 4
    • 0024285807 scopus 로고
    • Evidence from base-pair kinetics for two types of adenine tract structures in solution: Their relation to DNA curvature
    • Leroy, J. L., Charretier, E., Kochoyan, M., and Gueron, M. (1988) Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature Biochemistry 27, 8894-8898
    • (1988) Biochemistry , vol.27 , pp. 8894-8898
    • Leroy, J.L.1    Charretier, E.2    Kochoyan, M.3    Gueron, M.4
  • 5
    • 0025194337 scopus 로고
    • Proton exchange and base pair opening kinetics in 5′- d(CGCGAATTCGCG)-3′ and related dodecamers
    • Moe, J. G. and Russu, I. M. (1990) Proton exchange and base pair opening kinetics in 5′-d(CGCGAATTCGCG)-3′ and related dodecamers Nucleic Acids Res. 18, 821-827
    • (1990) Nucleic Acids Res. , vol.18 , pp. 821-827
    • Moe, J.G.1    Russu, I.M.2
  • 7
    • 0019331859 scopus 로고
    • RNA-DNA hybrid duplexes containing oligo (dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription
    • Martin, F. H. and Tinoco, I. J. (1980) RNA-DNA hybrid duplexes containing oligo (dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription Nucleic Acids Res. 8, 2295-2299
    • (1980) Nucleic Acids Res. , vol.8 , pp. 2295-2299
    • Martin, F.H.1    Tinoco, I.J.2
  • 8
    • 77649339290 scopus 로고    scopus 로고
    • Structural energetics of the adenine tract from an intrinsic transcription terminator
    • Huang, Y., Weng, X., and Russu, I. M. (2010) Structural energetics of the adenine tract from an intrinsic transcription terminator J. Mol. Biol. 397, 677-688
    • (2010) J. Mol. Biol. , vol.397 , pp. 677-688
    • Huang, Y.1    Weng, X.2    Russu, I.M.3
  • 9
    • 16644365966 scopus 로고    scopus 로고
    • Sequence-dependence of the energetics of opening of at base pairs in DNA
    • Chen, C. and Russu, I. M. (2004) Sequence-dependence of the energetics of opening of AT base pairs in DNA Biophys. J. 87, 1-7
    • (2004) Biophys. J. , vol.87 , pp. 1-7
    • Chen, C.1    Russu, I.M.2
  • 10
    • 33845555707 scopus 로고
    • Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences
    • Plateau, P. and Gueron, M. (1982) Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences J. Am. Chem. Soc. 104, 7310-7311
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 7310-7311
    • Plateau, P.1    Gueron, M.2
  • 11
    • 0029338320 scopus 로고
    • Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC(FHSQC) detection scheme that avoids water saturation
    • Mori, S., Abeygunawardana, C., Johnson, M. O., and van Zijl, P. C. M. (1995) Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC(FHSQC) detection scheme that avoids water saturation J. Magn. Reson. B 108, 94-98
    • (1995) J. Magn. Reson. B , vol.108 , pp. 94-98
    • Mori, S.1    Abeygunawardana, C.2    Johnson, M.O.3    Van Zijl, P.C.M.4
  • 12
    • 0000389264 scopus 로고
    • Use of a water flip-back pulse in the homonuclear NOESY experiment
    • Lippens, G., Dhalluin, C., and Wieruszeski, J.-M. (1995) Use of a water flip-back pulse in the homonuclear NOESY experiment J. Biomol. NMR 5, 327-331
    • (1995) J. Biomol. NMR , vol.5 , pp. 327-331
    • Lippens, G.1    Dhalluin, C.2    Wieruszeski, J.-M.3
  • 13
    • 1542269098 scopus 로고    scopus 로고
    • Probing Site-Specific Energetics in Proteins and Nucleic Acids by Hydrogen Exchange and Nuclear Magnetic Resonance Spectroscopy
    • DOI 10.1016/S0076-6879(04)79009-6
    • Russu, I. M. (2004) Probing site-specific energetics in proteins and nucleic acids by hydrogen exchange and NMR spectroscopy Methods Enzymol. 379, 152-175 (Pubitemid 38313471)
    • (2004) Methods in Enzymology , vol.379 , pp. 152-175
    • Russu, I.M.1
  • 14
    • 0020855355 scopus 로고
    • Hydrogen exchange and structural dynamics of proteins and nucleic acids
    • Englander, S. W. and Kallenbach, N. R. (1984) Hydrogen exchange and structural dynamics of proteins and nucleic acids Q. Rev. Biophys. 16, 521-655
    • (1984) Q. Rev. Biophys. , vol.16 , pp. 521-655
    • Englander, S.W.1    Kallenbach, N.R.2
  • 15
    • 0028864424 scopus 로고
    • Studies of base pair kinetics by NMR measurement of proton exchange
    • Gueron, M. and Leroy, J.-L. (1995) Studies of base pair kinetics by NMR measurement of proton exchange Methods Enzymol. 261, 383-413
    • (1995) Methods Enzymol. , vol.261 , pp. 383-413
    • Gueron, M.1    Leroy, J.-L.2
  • 16
    • 66149094661 scopus 로고    scopus 로고
    • Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids
    • Huang, Y., Chen, C., and Russu, I. M. (2009) Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids Biochemistry 48, 3988-3997
    • (2009) Biochemistry , vol.48 , pp. 3988-3997
    • Huang, Y.1    Chen, C.2    Russu, I.M.3
  • 18
    • 0026737976 scopus 로고
    • Kinetics and energetics of base-pair opening in 5′-d(CGCGAATTCGCG)- 3′ and a substituted dodecamer containing G•T mismatches
    • Moe, J. G. and Russu, I. M. (1992) Kinetics and energetics of base-pair opening in 5′-d(CGCGAATTCGCG)-3′ and a substituted dodecamer containing G•T mismatches Biochemistry 31, 8421-8428
    • (1992) Biochemistry , vol.31 , pp. 8421-8428
    • Moe, J.G.1    Russu, I.M.2
  • 19
    • 0040184162 scopus 로고    scopus 로고
    • Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: Evidence for a secondary long-lived open state of the base pair
    • DOI 10.1021/bi991863b
    • Warmlander, S., Sen, A., and Leijon, M. (2000) Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: evidence for a secondary long-lived open state of the base pair Biochemistry 39, 607-615 (Pubitemid 30077635)
    • (2000) Biochemistry , vol.39 , Issue.3 , pp. 607-615
    • Warmlander, S.1    Sen, A.2    Leijon, M.3
  • 20
    • 0035979354 scopus 로고    scopus 로고
    • Imino proton exchange and base-pair kinetics in RNA duplexes
    • DOI 10.1021/bi010385d
    • Snoussi, K. and Leroy, J.-L. (2001) Imino proton exchange and base-pair kinetics in RNA duplexes Biochemistry 40, 8898-8904 (Pubitemid 32709523)
    • (2001) Biochemistry , vol.40 , Issue.30 , pp. 8898-8904
    • Snoussi, K.1    Leroy, J.-L.2
  • 21
    • 0037178070 scopus 로고    scopus 로고
    • Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations
    • DOI 10.1021/ja025980x
    • Varnai, P. and Lavery, R. (2002) Base flipping in DNA: pathways and energetics studied with molecular dynamics simulations J. Am. Chem. Soc. 124, 7272-7273 (Pubitemid 34670427)
    • (2002) Journal of the American Chemical Society , vol.124 , Issue.25 , pp. 7272-7273
    • Varnai, P.1    Lavery, R.2
  • 22
    • 0037335588 scopus 로고    scopus 로고
    • Base pair opening within B-DNA: Free energy pathways for GC and AT pairs from umbrella sampling simulations
    • DOI 10.1093/nar/gkg239
    • Giudice, E., Varnai, P., and Lavery, R. (2003) Base pair opening within B-DNA: free energy pathways for GC and AT base pairs from umbrella sampling simulations Nucleic Acids Res. 31, 1434-1443 (Pubitemid 36304905)
    • (2003) Nucleic Acids Research , vol.31 , Issue.5 , pp. 1434-1443
    • Giudice, E.1    Varnai, P.2    Lavery, R.3
  • 23
    • 33644622321 scopus 로고    scopus 로고
    • Computational approaches for investigating base flipping in oligonucleotides
    • Priyakumar, U. D. and MacKerell, A. D., Jr. (2006) Computational approaches for investigating base flipping in oligonucleotides Chem. Rev. 106, 489-505
    • (2006) Chem. Rev. , vol.106 , pp. 489-505
    • Priyakumar, U.D.1    Mackerell Jr., A.D.2
  • 24
    • 0023513912 scopus 로고
    • The structure of an oligo(dA)·oligo(dT) tract and its biological implications
    • DOI 10.1038/330221a0
    • Nelson, H. C. M., Finch, J. T., Luisi, B. F., and Klug, A. (1987) The structure of an oligo(dA)•oligo(dT) tract and its biological implications Nature 330, 221-226 (Pubitemid 18006417)
    • (1987) Nature , vol.330 , Issue.6145 , pp. 221-226
    • Nelson, H.C.M.1    Finch, J.T.2    Luisi, B.F.3    Klug, A.4
  • 25
    • 0027203669 scopus 로고
    • A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend
    • DOI 10.1006/jmbi.1993.1349
    • DiGabriele, A. D. and Steitz, T. A. (1993) A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend J. Mol. Biol. 231, 1024-1039 (Pubitemid 23209877)
    • (1993) Journal of Molecular Biology , vol.231 , Issue.4 , pp. 1024-1039
    • DiGabriele, A.D.1    Steitz, T.A.2
  • 28
    • 0023494886 scopus 로고
    • A bifurcated hydrogen-bonded conformation in the d(A•T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin
    • Coll, M., Frederick, C. A., Wang, A. H.-J., and Rich, A. (1987) A bifurcated hydrogen-bonded conformation in the d(A•T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin Proc. Natl. Acad. Sci. U.S.A. 84, 8385-8389
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 8385-8389
    • Coll, M.1    Frederick, C.A.2    Wang, A.H.-J.3    Rich, A.4
  • 29
    • 0028904989 scopus 로고
    • Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2′-hydroxyl effects
    • Wang, S. and Kool, E. T. (1995) Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2′-hydroxyl effects Biochemistry 34, 4125-4132
    • (1995) Biochemistry , vol.34 , pp. 4125-4132
    • Wang, S.1    Kool, E.T.2
  • 30
    • 0037047422 scopus 로고    scopus 로고
    • The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA
    • DOI 10.1074/jbc.M202989200
    • Warmlander, S., Sponer, J. E., Sponer, J., and Leijon, M. (2002) The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA J. Biol. Chem. 277, 28491-28497 (Pubitemid 41079274)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.32 , pp. 28491-28497
    • Warmlander, S.1    Sponer, J.E.2    Sponer, J.3    Leijoni, M.4
  • 31
    • 77953293106 scopus 로고    scopus 로고
    • A′-form RNA helices are required for cytoplasmic mRNA transport in Drosophila
    • Bullock, S. L., Ringel, I., Ish-Horowicz, D., and Lukavsky, P. J. (2010) A′-form RNA helices are required for cytoplasmic mRNA transport in Drosophila Nat. Struct. Mol. Biol. 17, 703-710
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 703-710
    • Bullock, S.L.1    Ringel, I.2    Ish-Horowicz, D.3    Lukavsky, P.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.